Transcriptional profiling of biomass degradation-related genes during Trichoderma reesei growth on different carbon sources

Chen, Xiuzhen; Luo, Yingfeng; Yu, Hongtao; Sun, Yuhui; Wu, Hong; Song, Shuhui; Hu, Songnian; Dong, Zhiyang

doi:10.1016/j.jbiotec.2014.01.011

Cited by 18 publications

(17 citation statements)

References 26 publications

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“…To investigate the pattern behind the regulation of gene expression of these enzyme classes, studies conducted genome-wide analyses of the fungal transcriptome using several different techniques. These included RNA sequencing [50, 104, 122–125], microarray analysis [42, 126–129], and quantitative PCR [123, 130–132]. The protein abundance in the secretome was further analyzed and quantified by mass spectrometry [94, 101, 125, 131–135].…”

Section: Effect Of the Substrate Characteristics On The Fungal Transcmentioning

confidence: 99%

The influence of feedstock characteristics on enzyme production in Trichoderma reesei: a review on productivity, gene regulation and secretion profiles

Novy

Nielsen

Schink

et al. 2019

Biotechnol Biofuels

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Biorefineries, designed for the production of lignocellulose-based chemicals and fuels, are receiving increasing attention from the public, governments, and industries. A major obstacle for biorefineries to advance to commercial scale is the high cost of the enzymes required to derive the fermentable sugars from the feedstock used. As summarized in this review, techno-economic studies suggest co-localization and integration of enzyme manufacturing with the cellulosic biorefinery as the most promising alternative to alleviate this problem. Thus, cultivation of Trichoderma reesei, the principal producer of lignocellulolytic enzymes, on the lignocellulosic biomass processed on-site can reduce the cost of enzyme manufacturing. Further, due to a complex gene regulation machinery, the fungus can adjust the gene expression of the lignocellulolytic enzymes towards the characteristics of the feedstock, increasing the hydrolytic efficiency of the produced enzyme cocktail. Despite extensive research over decades, the underlying regulatory mechanisms are not fully elucidated. One aspect that has received relatively little attention in literature is the influence the characteristics of a lignocellulosic substrate, i.e., its chemical and physical composition, has on the produced enzyme mixture. Considering that the fungus is dependent on efficient enzymatic degradation of the lignocellulose for continuous supply of carbon and energy, a relationship between feedstock characteristics and secretome composition can be expected. The aim of this review was to systematically collect, appraise, and aggregate data and integrate results from studies analyzing enzyme production by T. reesei on insoluble cellulosic model substrates and lignocellulosic biomass. The results show that there is a direct effect of the substrate’s complexity (rated by structure, composition of the lignin–carbohydrate complex, and recalcitrance in enzymatic saccharification) on enzyme titers and the composition of specific activities in the secretome. It further shows that process-related factors, such as substrate loading and cultivation set-up, are direct targets for increasing enzyme yields. The literature on transcriptome and secretome composition further supports the proposed influence of substrate-related factors on the expression of lignocellulolytic enzymes. This review provides insights into the interrelation between the characteristics of the substrate and the enzyme production by T. reesei, which may help to advance integrated enzyme manufacturing of substrate-specific enzymes cocktails at scale.

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Section: Effect Of the Substrate Characteristics On The Fungal Transcmentioning

confidence: 99%

The influence of feedstock characteristics on enzyme production in Trichoderma reesei: a review on productivity, gene regulation and secretion profiles

Novy

Nielsen

Schink

et al. 2019

Biotechnol Biofuels

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“…Gene expression of CAZymes in Trichoderma has already achieved considerable attention in several genome-wide studies using microarrays or expressed sequence tag (EST)-based approaches (328,(340)(341)(342)(343).…”

Section: Cazymesmentioning

confidence: 99%

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Schmoll

Dattenböck

Carreras-Villaseñor

et al. 2016

Microbiol Mol Biol Rev

164

195

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SUMMARYThe genusTrichodermacontains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for “hot topic” research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism inT. reesei,T. atroviride, andT. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of eachTrichodermaspecies discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved inN-linked glycosylation was detected, as were indications for the ability ofTrichodermaspp. to generate hybrid galactose-containingN-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique toTrichoderma, and these warrant further investigation. We found interesting expansions in theTrichodermagenus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique toT. atrovirideis the duplication of the alternative sulfur amino acid synthesis pathway.

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“…Four of these putative transporters, TrSTR2, TrSTR3, TrSTR4, and TrSTR5, are highly similar to the reported disaccharide transporters in their amino acid sequences and the remaining transporter, TrSTR1, shows highly homologous with monosaccharide transporters. Here, we focused on the TrSTR1 protein because the Trstr1 gene (Trire2:50894) was apparently up-regulated with different carbon sources in comparison with glucose [10,18,19]. The phylogenetic tree ( Fig.…”

Section: Identification Of a Putative Sugar Transporter In T Reesei mentioning

confidence: 99%

A novel major facilitator transporter TrSTR1 is essential for pentose utilization and involved in xylanase induction in Trichoderma reesei

Huang

Chen

Qin

et al. 2015

Biochemical and Biophysical Research Communications

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Transcriptional profiling of biomass degradation-related genes during Trichoderma reesei growth on different carbon sources

Cited by 18 publications

References 26 publications

The influence of feedstock characteristics on enzyme production in Trichoderma reesei: a review on productivity, gene regulation and secretion profiles

The influence of feedstock characteristics on enzyme production in Trichoderma reesei: a review on productivity, gene regulation and secretion profiles

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

A novel major facilitator transporter TrSTR1 is essential for pentose utilization and involved in xylanase induction in Trichoderma reesei

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